Biology subjects

Toupance, B.

Publications and source records attributed to Toupance, B..

4 recordsLinked to original sources

bioRxiv2026

The genetic legacy of archaic hominins in Central and Southeast Asia uncovers three distinct Denisovan populations

The sequencing of Neanderthal and Denisovan genomes has provided new insights into human evolution. Today, interactions between Neanderthals, Denisovans, and populations of European, East Asian, and Oceanian descent are well documented. However, neighboring regions such as Central and Southeast Asia remain understudied for archaic admixture despite their key geographic location and complex migration histories. To fill this gap, we investigate archaic ancestry in 16 populations from Central Asia and 14 from mainland Southeast Asia. Our results show that Neanderthal and Denisovan ancestry in these populations is of the same order of magnitude as in other Eurasian populations. However, although Denisovan ancestry accounts for less than 1% in mainland Asian populations, it originates from several admixture events involving different Denisovan populations. In particular, we find in Southeast Asia that Denisovan ancestry results from three distinct admixture events with three different Denisovan populations, highlighting the complexity of Denisovan contact with the ancestors of present-day Southeast Asian populations and providing new insights into the extensive geographic distribution of Denisovan populations.

evolutionary biology↗

bioRxiv2022

Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences

Cultural Transmission of Reproductive Success (CTRS) has been observed in many human populations as well as other animals. It consists in a positive correlation of non-genetic origin between the progeny size of parents and children. This correlation can result from various factors, such as the social influence of parents on their children, the increase of childrens survival through allocare from uncle and aunts, or the transmission of resources. Here, we study the evolution of genomic diversity through time under CTRS. We show that CTRS has a double impact on population genetics: (1) effective population size decreases when CTRS starts, mimicking a population contraction, and increases back to its original value when CTRS stops; (2) coalescent trees topologies are distorted under CTRS, with higher imbalance and higher number of polytomies. Under long-lasting CTRS, effective population size stabilises but the distortion of tree topology remains, which yields U-shaped Site Frequency Spectra (SFS) under constant population size. We show that this CTRS impact yields a bias in SFS-based demographic inference. Considering that CTRS was detected in numerous human and animal populations worldwide, one should be cautious that inferring population past histories from genomic data can be biased by this cultural process.

genetics↗

bioRxiv2020

Detection of sexually antagonistic transmission distortions in trio datasets

Sex dimorphisms are widespread in animals and plants, for morphological as well as physiological traits. Understanding the genetic basis of sex dimorphism and its evolution is crucial for understanding biological differences between the sexes. Genetic variants with sex-antagonistic effects on fitness are expected to segregate in populations at the early phases of sexual dimorphism emergence. Detecting such variants is notoriously difficult, and the few genome-scan methods employed so far have limited power and little specificity. Here, we propose a new framework to detect a signature of sexually antagonistic selection. We rely on trio datasets where sex-biased transmission distortions can be directly tracked from parents to offspring, and allows identifying signal of sexually antagonistic transmission distortions in genomic regions. We report the genomic location and recombination pattern surrounding 66 regions detected as potentially under sexually antagonist selection. We find an enrichment of genes associated with embryonic development within these regions. Last, we highlight two candidates regions for sexually antagonistic selection in humans.

evolutionary biology↗

bioRxiv2019

Complex genetic admixture histories reconstructed with Approximate Bayesian Computations

Admixture is a fundamental evolutionary process that has influenced genetic patterns in numerous species. Maximum-likelihood approaches based on allele frequencies and linkage-disequilibrium have been extensively used to infer admixture processes from dense genome-wide datasets mostly in human populations. Nevertheless, complex admixture histories, beyond one or two pulses of admixture, remain methodologically challenging to reconstruct, especially when large datasets are unavailable. We develop an Approximate Bayesian Computations (ABC) framework to reconstruct complex admixture histories from independent genetic markers. We built the software package MetHis to simulate independent SNPs in a two-way admixed population for scenarios with multiple admixture pulses, or monotonically decreasing or increasing admixture at each generation; drawing model-parameter values from prior distributions set by the user. For each simulated dataset, we calculate 24 summary statistics describing genetic diversity and moments of individual admixture fraction. We coupled MetHis with existing ABC algorithms and investigate the admixture history of an African American and a Barbadian population. Results show that Random-Forest ABC scenario-choice, followed by Neural-Network ABC posterior parameter estimation, can distinguish most complex admixture scenarios and provide accurate model-parameter estimations. For both admixed populations, we find that monotonically decreasing contributions over time, from the European and African sources, explain the observed data more accurately than multiple admixture pulses. Furthermore, we find contrasted trajectories of introgression decay from the European and African sources between the two admixed populations. This approach will allow for reconstructing detailed admixture histories in numerous populations and species, particularly when maximum-likelihood methods are intractable.

genetics↗